For my installation NOFMA suggest using a 1" 15 guage fully barbed brad. I cannot find a flooring gun that shoots this. I have a 15 guage finish brad nailer that will hold 1" brads, so can this be used?

What are you installing? I can't think of anything that would call for a 1" brad. Though I do a lot more gluing that nailing.

3/8 Cherry to 1/2" plywood over concrete.

Well I think you should be either adding another 1/4 inch of plywood, or gluing the floor down.
The only nailing process i can see possibly working is with a powernail #200 or #250 nailer, using 1 inch "E-cleats"
Using any kind of finishing nailer to install a whole floor would be an engineering feat to avoid any edge damage.

You are confusing the nailing recommendations with 5/16" FACE-NAILED flooring, which is square-edged. If your 3/8" flooring has a tongue and groove ( it should ) there are many nailers and staplers that will work. Read pg. 6 of NOFMA manual for proper nail size:

http://www.nofma.org/Portals/0/Publicat ... Floors.pdf

I have fastened the 1/2 plywood to the concrete and am debating whether or not to glue or nail. I have 5/16 expantion joints in the plywood, could I still glue this down or does that limit me to nailing?

The floor will span the expansion gaps with no problem, if you decide to glue.

Thanks. The reason why I ask is I realized I screwed up by putting 1/2 down instead of 3/4 so my 1" staple will protrude through the 1/2 subfloor onto the concrete.
I dont mind taking up the 1/2 and putting down 3/4 if stapling is a better option.
What do you think

Why waste the 1/2 inch that is already there, just add a layer of 1/4 inch on top

Exactly! Just add more plywood. 1/4 to 3/8".